Hi Niels,

The NITRC forum somehow suppressed the response I had written in my previous post. So here I go again. First thanks for posting that comment. Facilitating the involvement of people like you is part of what we're trying to achieve. Regarding your question on an easy way to get started, given your profile I would suggest to look into SPM :
http://www.fil.ion.ucl.ac.uk/spm/
It has a good documentation and comes with a reader/writer for NIFTI (neuroimaging volumes) in matlab. The Athena release has a spatial resolution that is low enough to process a full brain connectivity matrix, if you restrict the analysis to grey matter (the grey matter mask comes with the release).

Otherwise, you may want to wait for us to release the parcelation results, i.e. .mat files with time x space arrays, each time course being an average on a small (spatially connex) region of interest. This release will come very soon. We'll have two methods (Craddock et al., HBM In Press)/(Bellec et al., Neuroimage 2006) and multiple resolutions (from 200 to 3000 ROIs). You'll be able to load those variables as well as the regions in matlab and start working "out of the box". I expect that the whole database will not be bigger than a couple 100 of Mbs in that format.

As of graph visualization tools, you have tools in Matlab/python, and there are several open-source specialized projects such as graphviz and gephi
http://www.graphviz.org/
http://www.slideshare.net/gephi/gephi-exploratory-networks-analysis-software-4931589

I hope this helps, good luck with your analysis.

Pierre